Tbp (TATA box binding protein) - Rat Genome Database

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Gene: Tbp (TATA box binding protein) Rattus norvegicus
Analyze
Symbol: Tbp
Name: TATA box binding protein
RGD ID: 67398
Description: Enables DNA binding activity. Contributes to RNA polymerase II general transcription initiation factor activity. Involved in positive regulation of DNA-templated transcription and spermatogenesis. Located in nucleus. Part of transcription factor TFIID complex. Human ortholog(s) of this gene implicated in late onset Parkinson's disease; schizophrenia; spinocerebellar ataxia type 17; and type 1 diabetes mellitus. Orthologous to human TBP (TATA-box binding protein); PARTICIPATES IN cisplatin drug pathway; RNA polymerase I transcription pathway; RNA polymerase II transcription initiation pathway; INTERACTS WITH 2,4-dinitrotoluene; fipronil; thioacetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC93994; TATA-box-binding protein; TFIID
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2156,463,330 - 56,480,430 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl156,463,618 - 56,510,016 (+)Ensembl
Rnor_6.0157,491,381 - 57,509,335 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl157,491,643 - 57,508,449 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,419,943 - 58,438,618 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,390,756 - 54,407,563 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,393,700 - 54,410,507 (+)NCBI
Celera152,668,920 - 52,685,703 (+)NCBICelera
Cytogenetic Map1q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. TIP120B: a novel TIP120-family protein that is expressed specifically in muscle tissues. Aoki T, etal., Biochem Biophys Res Commun 1999 Aug 11;261(3):911-6.
2. Expanded trinucleotide repeats in the TBP/SCA17 gene mapped to chromosome 6q27 are associated with schizophrenia. Chen CM, etal., Schizophr Res. 2005 Oct 15;78(2-3):131-6.
3. increased Expression of TBP/TFIID after spinal cord injury in adult rats. Ding T, etal., Cell Mol Neurobiol. 2014 Jul;34(5):669-77. doi: 10.1007/s10571-014-0048-7. Epub 2014 Apr 8.
4. Cell growth- and differentiation-dependent regulation of RNA polymerase III transcription. Dumay-Odelot H, etal., Cell Cycle. 2010 Sep 15;9(18):3687-99. Epub 2010 Sep 1.
5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
7. Structural insights into transcription initiation by RNA polymerase II. Grunberg S and Hahn S, Trends Biochem Sci. 2013 Dec;38(12):603-11. doi: 10.1016/j.tibs.2013.09.002. Epub 2013 Oct 11.
8. Neuronal expression of TATA box-binding protein containing expanded polyglutamine in knock-in mice reduces chaperone protein response by impairing the function of nuclear factor-Y transcription factor. Huang S, etal., Brain. 2011 Jul;134(Pt 7):1943-58.
9. Isolation of rat TATA factor as an active 75kDa protein complex. Igarashi A, etal., Biochem Biophys Res Commun. 1994 Nov 15;204(3):1125-30.
10. A novel transgenic rat model for spinocerebellar ataxia type 17 recapitulates neuropathological changes and supplies in vivo imaging biomarkers. Kelp A, etal., J Neurosci. 2013 May 22;33(21):9068-81. doi: 10.1523/JNEUROSCI.5622-12.2013.
11. TFIIB-related factors in RNA polymerase I transcription. Knutson BA and Hahn S, Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):265-73. doi: 10.1016/j.bbagrm.2012.08.003. Epub 2012 Aug 30.
12. Structural bioinformatics of the general transcription factor TFIID. Malkowska M, etal., Biochimie. 2013 Apr;95(4):680-91. doi: 10.1016/j.biochi.2012.10.024. Epub 2012 Nov 9.
13. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
14. SCA17, a novel autosomal dominant cerebellar ataxia caused by an expanded polyglutamine in TATA-binding protein. Nakamura K, etal., Hum Mol Genet. 2001 Jul 1;10(14):1441-8.
15. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
16. Association of a CAG/CAA repeat sequence in the TBP gene with type I diabetes. Owerbach D, etal., Biochem Biophys Res Commun. 2004 Oct 22;323(3):865-9.
17. No evidence for association of the TATA-box binding protein glutamine repeat sequence or the flanking chromosome 6q27 region with type 1 diabetes. Payne F, etal., Biochem Biophys Res Commun. 2005 Jun 3;331(2):435-41.
18. Transcription of the TATA binding protein gene is highly up-regulated during spermatogenesis. Persengiev SP, etal., Mol Endocrinol. 1996 Jun;10(6):742-7.
19. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
20. Hepatitis C virus NS5A protein binds TBP and p53, inhibiting their DNA binding and p53 interactions with TBP and ERCC3. Qadri I, etal., Biochim Biophys Acta. 2002 Oct 21;1592(2):193-204.
21. TBP, a polyglutamine tract containing protein, accumulates in Alzheimer's disease. Reid SJ, etal., Brain Res Mol Brain Res. 2004 Jun 18;125(1-2):120-8.
22. An integrated rat genetic map: analysis of linkage conservation with the mouse and human maps. Remmers EF, etal., Transplant Proc 1999 May;31(3):1549-54.
23. GOA pipeline RGD automated data pipeline
24. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
25. The presence of TATA-binding protein in the brainstem, correlated with sleep apnea in SIDS victims. Sawaguchi T, etal., Early Hum Dev. 2003 Dec;75 Suppl:S109-18.
26. Fundamental cellular processes do not require vertebrate-specific sequences within the TATA-binding protein. Schmidt EE, etal., J Biol Chem 2003 Feb 21;278(8):6168-74. Epub 2002 Dec 5.
27. RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation. Schneider DA Gene. 2012 Feb 10;493(2):176-84. doi: 10.1016/j.gene.2011.08.006. Epub 2011 Aug 26.
28. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
29. Inhibition of transcription by platinum antitumor compounds. Todd RC and Lippard SJ, Metallomics. 2009;1(4):280-91. doi: 10.1039/b907567d.
30. Insoluble TATA-binding protein accumulation in Huntington's disease cortex. van Roon-Mom WM, etal., Brain Res Mol Brain Res. 2002 Dec 30;109(1-2):1-10.
31. A structural perspective on RNA polymerase I and RNA polymerase III transcription machineries. Vannini A Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):258-64. doi: 10.1016/j.bbagrm.2012.09.009. Epub 2012 Sep 29.
32. Selective alterations of transcription factors in MPP+-induced neurotoxicity in PC12 cells. Xu Z, etal., Neurotoxicology. 2005 Aug;26(4):729-37.
33. Molecular cloning of a novel 120-kDa TBP-interacting protein. Yogosawa S, etal., Biochem Biophys Res Commun 1996 Dec 13;229(2):612-7.
34. Association of the rat heterogeneous nuclear RNA-ribonucleoprotein F with TATA-binding protein. Yoshida T, etal., FEBS Lett 1999 Aug 27;457(2):251-4.
Additional References at PubMed
PMID:7724559   PMID:7729427   PMID:7933101   PMID:8626665   PMID:9027316   PMID:9722567   PMID:9841876   PMID:10526239   PMID:11005381   PMID:11861477   PMID:12411709   PMID:12665565  
PMID:12676957   PMID:14580349   PMID:15601870   PMID:15641800   PMID:15927180   PMID:16263792   PMID:16522640   PMID:16540471   PMID:16822332   PMID:17242199   PMID:17641088   PMID:18218637  
PMID:18722179   PMID:18838386   PMID:19235719   PMID:19861239   PMID:21245044   PMID:22194471   PMID:22323595   PMID:24289924   PMID:25336585   PMID:26638071   PMID:27007846   PMID:27193682  
PMID:27923787   PMID:28134789  


Genomics

Comparative Map Data
Tbp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2156,463,330 - 56,480,430 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl156,463,618 - 56,510,016 (+)Ensembl
Rnor_6.0157,491,381 - 57,509,335 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl157,491,643 - 57,508,449 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0158,419,943 - 58,438,618 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,390,756 - 54,407,563 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,393,700 - 54,410,507 (+)NCBI
Celera152,668,920 - 52,685,703 (+)NCBICelera
Cytogenetic Map1q12NCBI
TBP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386170,554,369 - 170,572,859 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6170,554,302 - 170,572,870 (+)EnsemblGRCh38hg38GRCh38
GRCh376170,863,457 - 170,881,947 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366170,705,396 - 170,723,872 (+)NCBINCBI36hg18NCBI36
Build 346170,781,102 - 170,799,578NCBI
Celera6171,658,683 - 171,677,210 (+)NCBI
Cytogenetic Map6q27NCBI
HuRef6168,368,477 - 168,387,004 (+)NCBIHuRef
CHM1_16171,124,696 - 171,144,174 (+)NCBICHM1_1
T2T-CHM13v2.06171,927,920 - 171,946,405 (+)NCBI
Tbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391715,720,150 - 15,737,689 (+)NCBIGRCm39mm39
GRCm39 Ensembl1715,720,150 - 15,748,641 (+)Ensembl
GRCm381715,499,888 - 15,517,427 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1715,499,888 - 15,528,379 (+)EnsemblGRCm38mm10GRCm38
MGSCv371715,636,852 - 15,654,391 (+)NCBIGRCm37mm9NCBIm37
MGSCv361715,208,038 - 15,221,746 (+)NCBImm8
Celera1716,285,165 - 16,302,716 (+)NCBICelera
Cytogenetic Map17A2NCBI
cM Map178.95NCBI
Tbp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554113,268,147 - 3,285,077 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554113,268,147 - 3,285,567 (-)NCBIChiLan1.0ChiLan1.0
TBP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16173,800,204 - 173,818,744 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6173,800,240 - 173,826,909 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06168,714,214 - 168,732,744 (+)NCBIMhudiblu_PPA_v0panPan3
TBP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11272,458,959 - 72,479,271 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1272,459,041 - 72,479,124 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1272,221,201 - 72,241,583 (+)NCBI
ROS_Cfam_1.01273,444,412 - 73,464,611 (+)NCBI
ROS_Cfam_1.0 Ensembl1273,441,852 - 73,464,514 (+)Ensembl
UMICH_Zoey_3.11272,717,146 - 72,737,106 (+)NCBI
UNSW_CanFamBas_1.01272,539,334 - 72,559,523 (+)NCBI
UU_Cfam_GSD_1.01272,930,358 - 72,950,554 (+)NCBI
Tbp
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946151,203,571 - 151,222,342 (-)NCBI
SpeTri2.0NW_00493709846,572 - 65,304 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.115,669 - 23,675 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TBP
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11397,661,905 - 97,678,640 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1397,660,864 - 97,681,497 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604069,659,919 - 69,679,427 (-)NCBIVero_WHO_p1.0
Tbp
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248506,359,418 - 6,375,391 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248506,359,382 - 6,375,391 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Tbp  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2156,467,687 - 56,467,977 (+)MAPPERmRatBN7.2
Rnor_6.0157,495,713 - 57,496,002NCBIRnor6.0
Rnor_5.0158,424,271 - 58,424,560UniSTSRnor5.0
RGSC_v3.4154,394,826 - 54,395,115UniSTSRGSC3.4
Celera152,672,990 - 52,673,279UniSTS
Cytogenetic Map1q12UniSTS
Tbp  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2156,480,048 - 56,480,246 (+)MAPPERmRatBN7.2
Rnor_6.0157,508,071 - 57,508,268NCBIRnor6.0
Rnor_5.0158,438,183 - 58,438,380UniSTSRnor5.0
Celera152,685,324 - 52,685,521UniSTS
Cytogenetic Map1q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:96
Count of miRNA genes:64
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000002038
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 26 33 18 19 18 1 1 74 27 41 11 1
Low 17 24 23 23 7 10 8 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002038   ⟹   ENSRNOP00000002038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl156,463,618 - 56,480,427 (+)Ensembl
Rnor_6.0 Ensembl157,491,643 - 57,508,449 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105252   ⟹   ENSRNOP00000088616
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl156,463,618 - 56,491,438 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106038   ⟹   ENSRNOP00000091348
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl156,463,618 - 56,480,427 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114159   ⟹   ENSRNOP00000080115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl156,463,618 - 56,489,745 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118785   ⟹   ENSRNOP00000077324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl156,463,618 - 56,510,016 (+)Ensembl
RefSeq Acc Id: NM_001004198   ⟹   NP_001004198
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2156,463,618 - 56,480,428 (+)NCBI
Rnor_6.0157,491,643 - 57,508,450 (+)NCBI
Rnor_5.0158,419,943 - 58,438,618 (+)NCBI
RGSC_v3.4154,390,756 - 54,407,563 (+)RGD
Celera152,668,920 - 52,685,703 (+)RGD
Sequence:
RefSeq Acc Id: XM_006227980   ⟹   XP_006228042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2156,463,330 - 56,480,430 (+)NCBI
Rnor_6.0157,491,381 - 57,509,335 (+)NCBI
Rnor_5.0158,419,943 - 58,438,618 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001004198 (Get FASTA)   NCBI Sequence Viewer  
  XP_006228042 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81939 (Get FASTA)   NCBI Sequence Viewer  
  EDL99816 (Get FASTA)   NCBI Sequence Viewer  
  EDL99817 (Get FASTA)   NCBI Sequence Viewer  
  EDL99818 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001004198   ⟸   NM_001004198
- UniProtKB: Q66HB1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006228042   ⟸   XM_006227980
- Peptide Label: isoform X1
- UniProtKB: Q66HB1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002038   ⟸   ENSRNOT00000002038
RefSeq Acc Id: ENSRNOP00000080115   ⟸   ENSRNOT00000114159
RefSeq Acc Id: ENSRNOP00000088616   ⟸   ENSRNOT00000105252
RefSeq Acc Id: ENSRNOP00000077324   ⟸   ENSRNOT00000118785
RefSeq Acc Id: ENSRNOP00000091348   ⟸   ENSRNOT00000106038

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66HB1-F1-model_v2 AlphaFold Q66HB1 1-318 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13689646
Promoter ID:EPDNEW_R170
Type:single initiation site
Name:Tbp_1
Description:TATA box binding protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0157,491,634 - 57,491,694EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:67398 AgrOrtholog
BioCyc Gene G2FUF-61309 BioCyc
Ensembl Genes ENSRNOG00000001489 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002038 ENTREZGENE
  ENSRNOP00000002038.3 UniProtKB/TrEMBL
  ENSRNOP00000077324.1 UniProtKB/TrEMBL
  ENSRNOP00000080115.1 UniProtKB/TrEMBL
  ENSRNOP00000088616.1 UniProtKB/TrEMBL
  ENSRNOP00000091348.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002038 ENTREZGENE
  ENSRNOT00000002038.5 UniProtKB/TrEMBL
  ENSRNOT00000105252.1 UniProtKB/TrEMBL
  ENSRNOT00000106038.1 UniProtKB/TrEMBL
  ENSRNOT00000114159.1 UniProtKB/TrEMBL
  ENSRNOT00000118785.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.310.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7115389 IMAGE-MGC_LOAD
InterPro TBP UniProtKB/TrEMBL
  TBP_CS UniProtKB/TrEMBL
  TBP_dom_sf UniProtKB/TrEMBL
  TBP_eukaryotic UniProtKB/TrEMBL
KEGG Report rno:117526 UniProtKB/TrEMBL
MGC_CLONE MGC:93994 IMAGE-MGC_LOAD
NCBI Gene 117526 ENTREZGENE
PANTHER TBP UniProtKB/TrEMBL
Pfam TBP UniProtKB/TrEMBL
PhenoGen Tbp PhenoGen
PRINTS TIFACTORIID UniProtKB/TrEMBL
PROSITE TFIID UniProtKB/TrEMBL
UniProt A0A8I5Y1F6_RAT UniProtKB/TrEMBL
  A0A8I5ZNX4_RAT UniProtKB/TrEMBL
  A0A8I6A9T0_RAT UniProtKB/TrEMBL
  A0A8I6AFF5_RAT UniProtKB/TrEMBL
  Q66HB1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Tbp  TATA box binding protein      Symbol and Name status set to approved 70586 APPROVED
2001-10-25 Tbp  TATA box binding protein      Name updated 68916 RESERVED

RGD Curation Notes
Note Type Note Reference
gene_function binds specifically to the TATA box promoter element which lies close to the position of transcription initiation 1299882
gene_process plays a role in the activation of eukaryotic genes transcribed by DNA polymerase II 1299882